def setup_plot_widgets(self):
self.peakmap_plotter = PeakMapPlottingWidget()
self.peakmap_plotter.set_peakmaps(self.peakmap, self.peakmap2)
self.eic_plotter = EicPlottingWidget(with_range=False)
self.mz_plotter = MzPlottingWidget()
self.peakmap_plotter.set_logarithmic_scale(1)
self.peakmap_plotter.set_gamma(self.gamma)
self.eic_plotter.set_overall_range(self.rtmin, self.rtmax)
self.mz_plotter.set_overall_range(self.mzmin, self.mzmax)
def setup_plot_widgets(self):
self.peakmap_plotter = PeakMapPlottingWidget()
self.peakmap_plotter.set_peakmaps(self.peakmap, self.peakmap2)
self.eic_plotter = EicPlottingWidget(with_range=False)
self.mz_plotter = MzPlottingWidget()
self.peakmap_plotter.set_logarithmic_scale(1)
self.peakmap_plotter.set_gamma(self.gamma)
self.eic_plotter.set_overall_range(self.rtmin, self.rtmax)
self.mz_plotter.set_overall_range(self.mzmin, self.mzmax)
class PeakMapExplorer(EmzedDialog):
def __init__(self, ok_rows_container=[], parent=None):
super(PeakMapExplorer, self).__init__(parent)
self.setWindowFlags(Qt.Window)
# Destroying the C++ object right after closing the dialog box,
# otherwise it may be garbage-collected in another QThread
# (e.g. the editor's analysis thread in Spyder), thus leading to
# a segmentation fault on UNIX or an application crash on Windows
self.ok_rows = ok_rows_container
self.setAttribute(Qt.WA_DeleteOnClose)
self.setWindowFlags(Qt.Window)
self.gamma = 3.0
self.last_used_directory_for_load = None
self.last_used_directory_for_save = None
self.history = History()
def keyPressEvent(self, e):
# avoid closing of dialog when Esc key pressed:
if e.key() != Qt.Key_Escape:
return super(PeakMapExplorer, self).keyPressEvent(e)
def setWindowTitle(self):
if self.peakmap2 is None:
title = os.path.basename(self.peakmap.meta.get("source", ""))
else:
p1 = os.path.basename(self.peakmap.meta.get("source", ""))
p2 = os.path.basename(self.peakmap2.meta.get("source", ""))
title = "yellow=%s, blue=%s" % (p1, p2)
super(PeakMapExplorer, self).setWindowTitle(title)
def setup(self, peakmap, peakmap2=None, table=None):
self.table = table
def collect_precursor_mz(pm):
for s in pm:
if s.precursors:
if s.msLevel > 1:
yield s.precursors[0][0]
self.ms_levels = set(peakmap.getMsLevels())
self.precursor_mz = set(collect_precursor_mz(peakmap))
if peakmap2 is not None:
self.ms_levels &= set(peakmap2.getMsLevels())
self.precursor_mz &= set(collect_precursor_mz(peakmap2))
self.ms_levels = sorted(self.ms_levels)
self.precursor_mz = sorted(self.precursor_mz)
self.setup_table_widgets()
self.setup_input_widgets()
self.history_list = QComboBox(self)
self.setup_ms2_widgets()
self.full_pm = peakmap
self.full_pm2 = peakmap2
self.dual_mode = self.full_pm2 is not None
self.current_ms_level = self.ms_levels[0]
self.process_peakmap(self.current_ms_level)
self.rtmin, self.rtmax, self.mzmin, self.mzmax = get_range(
self.peakmap, self.peakmap2)
self.setup_plot_widgets()
self.setup_menu_bar()
self.setup_layout()
self.connect_signals_and_slots()
self.setup_initial_values()
self.plot_peakmap()
def setup_ms2_widgets(self):
self.spectra_selector_widget.set_data(self.ms_levels,
self.precursor_mz)
def setup_table_widgets(self):
if self.table is not None:
self.table_widget = create_table_widget(self.table, self)
self.select_all_peaks = QPushButton("Select all peaks", self)
self.unselect_all_peaks = QPushButton("Unselect all peaks", self)
self.done_button = QPushButton("Done", self)
def setup_menu_bar(self):
self.menu_bar = QMenuBar(self)
menu = QMenu("Peakmap Explorer", self.menu_bar)
self.menu_bar.addMenu(menu)
if not self.dual_mode:
self.load_action = QAction("Load Peakmap", self)
self.load_action.setShortcut(QKeySequence("Ctrl+L"))
self.load_action2 = None
menu.addAction(self.load_action)
else:
self.load_action = QAction("Load Yellow Peakmap", self)
self.load_action2 = QAction("Load Blue Peakmap", self)
menu.addAction(self.load_action)
menu.addAction(self.load_action2)
self.save_action = QAction("Save selected range as image", self)
self.save_action.setShortcut(QKeySequence("Ctrl+S"))
menu.addAction(self.save_action)
menu = QMenu("Help", self.menu_bar)
self.help_action = QAction("Help", self)
self.help_action.setShortcut(QKeySequence("F1"))
menu.addAction(self.help_action)
self.menu_bar.addMenu(menu)
def process_peakmap(self, ms_level, pre_mz_min=None, pre_mz_max=None):
peakmap = self.full_pm.filter(lambda s: s.msLevel == ms_level)
if ms_level > 1 and pre_mz_min is not None:
peakmap = peakmap.filter(
lambda s: s.precursors[0][0] >= pre_mz_min)
if ms_level > 1 and pre_mz_max is not None:
peakmap = peakmap.filter(
lambda s: s.precursors[0][0] <= pre_mz_max)
if self.full_pm2 is not None:
peakmap2 = self.full_pm2.filter(lambda s: s.msLevel == ms_level)
self.peakmap = peakmap
if self.dual_mode:
self.peakmap2 = peakmap2
else:
self.peakmap2 = None
for i, msl in enumerate(self.ms_levels):
if msl == ms_level:
pass # TODO self.ms_level.setCurrentIndex(i)
self.setWindowTitle()
def setup_initial_values(self):
imax = self.peakmap_plotter.get_total_imax()
self.image_scaling_widget.set_max_intensity(imax)
self.image_scaling_widget.set_gamma(self.gamma)
self.view_range_widget.set_view_range(self.rtmin, self.rtmax,
self.mzmin, self.mzmax)
def setup_input_widgets(self):
self.image_scaling_widget = ImageScalingWidget(self)
self.spectra_selector_widget = SpectraSelectorWidget(self)
self.view_range_widget = ViewRangeWidget(self)
def setup_plot_widgets(self):
self.peakmap_plotter = PeakMapPlottingWidget()
self.peakmap_plotter.set_peakmaps(self.peakmap, self.peakmap2)
self.eic_plotter = EicPlottingWidget(with_range=False)
self.mz_plotter = MzPlottingWidget()
self.peakmap_plotter.set_logarithmic_scale(1)
self.peakmap_plotter.set_gamma(self.gamma)
self.eic_plotter.set_overall_range(self.rtmin, self.rtmax)
self.mz_plotter.set_overall_range(self.mzmin, self.mzmax)
def setup_layout(self):
outer_layout = QVBoxLayout()
outer_layout.addWidget(self.menu_bar)
outer_layout.setStretch(0, 1)
h_splitter = QSplitter(self)
h_splitter.setOrientation(Qt.Horizontal)
# FIRST COLUMN of h_splitter is chromatogram + peakmap: ############################
v_splitter1 = QSplitter(self)
v_splitter1.setOrientation(Qt.Vertical)
v_splitter1.addWidget(self.eic_plotter)
v_splitter1.addWidget(self.peakmap_plotter)
self.peakmap_plotter.setMinimumSize(250, 200)
v_splitter1.setStretchFactor(0, 1)
v_splitter1.setStretchFactor(1, 3)
h_splitter.addWidget(v_splitter1)
h_splitter.setStretchFactor(0, 2)
# SECOND COLUMN of h_splittier holds controlx boxes + mz plot #######################
v_splitter2 = QSplitter(self)
v_splitter2.setOrientation(Qt.Vertical)
v_splitter2.addWidget(self.image_scaling_widget)
v_splitter2.addWidget(self.spectra_selector_widget)
v_splitter2.addWidget(self.view_range_widget)
v_splitter2.addWidget(self.history_list)
v_splitter2.addWidget(self.mz_plotter)
v_splitter2.setStretchFactor(0, 0)
v_splitter2.setStretchFactor(1, 0)
v_splitter2.setStretchFactor(2, 0)
v_splitter2.setStretchFactor(3, 0)
v_splitter2.setStretchFactor(4, 1)
h_splitter.addWidget(v_splitter2)
h_splitter.setStretchFactor(1, 1)
# THIRD COLUMN of h_splittier holds control table + buttons ##########################
if self.table:
frame = QFrame(self)
layout = QVBoxLayout(frame)
frame.setLayout(layout)
layout.addWidget(self.table_widget)
button_row_layout = QHBoxLayout(frame)
button_row_layout.addWidget(self.select_all_peaks)
button_row_layout.addWidget(self.unselect_all_peaks)
button_row_layout.addWidget(self.done_button)
layout.addLayout(button_row_layout)
h_splitter.addWidget(frame)
h_splitter.setStretchFactor(2, 2)
outer_layout.addWidget(h_splitter)
self.setLayout(outer_layout)
outer_layout.setStretch(1, 99)
def connect_signals_and_slots(self):
self.image_scaling_widget.USE_LOG_SCALE.connect(self.use_logscale)
self.image_scaling_widget.GAMMA_CHANGED.connect(self.gamma_changed)
self.image_scaling_widget.IMIN_CHANGED.connect(self.set_image_min)
self.image_scaling_widget.IMAX_CHANGED.connect(self.set_image_max)
self.spectra_selector_widget.MS_LEVEL_CHOSEN.connect(
self.ms_level_chosen)
self.spectra_selector_widget.PRECURSOR_RANGE_CHANGED.connect(
self.set_precursor_range)
self.view_range_widget.RANGE_CHANGED.connect(self.update_image_range)
self.connect(self.history_list, SIGNAL("activated(int)"),
self.history_item_selected)
if self.dual_mode:
self.connect(self.load_action, SIGNAL("triggered()"),
self.do_load_yellow)
self.connect(self.load_action2, SIGNAL("triggered()"),
self.do_load_blue)
else:
self.connect(self.load_action, SIGNAL("triggered()"), self.do_load)
self.connect(self.save_action, SIGNAL("triggered()"), self.do_save)
self.connect(self.help_action, SIGNAL("triggered()"), self.show_help)
self.peakmap_plotter.NEW_IMAGE_LIMITS.connect(
self.image_limits_upated_by_user)
self.peakmap_plotter.KEY_LEFT.connect(
self.user_pressed_left_key_in_plot)
self.peakmap_plotter.KEY_RIGHT.connect(
self.user_pressed_right_key_in_plot)
self.peakmap_plotter.KEY_BACKSPACE.connect(
self.user_pressed_backspace_key_in_plot)
self.peakmap_plotter.KEY_END.connect(self.user_pressed_end_key_in_plot)
self.peakmap_plotter.CURSOR_MOVED.connect(self.cursor_moved_in_plot)
self.eic_plotter.CURSOR_MOVED.connect(self.eic_cursor_moved)
self.eic_plotter.VIEW_RANGE_CHANGED.connect(
self.eic_view_range_changed)
self.mz_plotter.CURSOR_MOVED.connect(self.mz_cursor_moved)
self.mz_plotter.VIEW_RANGE_CHANGED.connect(self.mz_view_range_changed)
if self.table is not None:
self.connect(self.table_widget.verticalHeader(),
SIGNAL("sectionClicked(int)"), self.row_selected)
self.connect(self.table_widget,
SIGNAL("itemClicked(QTableWidgetItem*)"),
self.cell_clicked)
self.connect(self.select_all_peaks, SIGNAL("pressed()"),
self.select_all_peaks_button_pressed)
self.connect(self.unselect_all_peaks, SIGNAL("pressed()"),
self.unselect_all_peaks_button_pressed)
self.connect(self.done_button, SIGNAL("pressed()"),
self.done_button_pressed)
def key_release_handler(evt):
tw = self.table_widget
active_rows = set(
ix.row()
for ix in tw.selectionModel().selection().indexes())
if active_rows:
row = active_rows.pop()
if evt.key() in (Qt.Key_Up, Qt.Key_Down):
tw.selectRow(row)
tw.verticalHeader().emit(SIGNAL("sectionClicked(int)"),
row)
return
return QTableWidget.keyPressEvent(tw, evt)
self.table_widget.keyReleaseEvent = key_release_handler
def cursor_moved_in_plot(self, rt, mz):
self.eic_plotter.set_cursor_pos(rt)
self.mz_plotter.set_cursor_pos(mz)
def eic_cursor_moved(self, rt):
self.peakmap_plotter.set_cursor_rt(rt)
def eic_view_range_changed(self, rtmin, rtmax):
"""
we want to avoid the loop EIC_RANGE_CHANGED -> VIEW_RANGE_CHANGED -> EIC_RANGE_CHANGED
and we do not want to fully block emitting of VIEW_RANGE_CHANGED.
so self.peakmap_plotter.blockSignals() does not work here, instead we "cut" the last
connection here:
"""
self.eic_plotter.VIEW_RANGE_CHANGED.disconnect()
self.peakmap_plotter.blockSignals(True)
self.peakmap_plotter.set_rt_limits(rtmin, rtmax)
self.peakmap_plotter.blockSignals(False)
self.peakmap_plotter.replot()
self.eic_plotter.VIEW_RANGE_CHANGED.connect(
self.eic_view_range_changed)
def mz_view_range_changed(self, mzmin, mzmax):
"""
we want to avoid the loop MZ_RANGE_CHANGED -> VIEW_RANGE_CHANGED -> MZ_RANGE_CHANGED
and we do not want to fully block emitting of VIEW_RANGE_CHANGED.
so self.peakmap_plotter.blockSignals() does not work here, instead we "cut" the last
connection here:
"""
self.mz_plotter.VIEW_RANGE_CHANGED.disconnect()
self.peakmap_plotter.blockSignals(True)
self.peakmap_plotter.set_mz_limits(mzmin, mzmax)
self.peakmap_plotter.blockSignals(False)
self.peakmap_plotter.replot()
self.mz_plotter.VIEW_RANGE_CHANGED.connect(self.mz_view_range_changed)
def mz_cursor_moved(self, mz):
self.peakmap_plotter.set_cursor_mz(mz)
def image_limits_upated_by_user(self, rtmin, rtmax, mzmin, mzmax):
self.update_peakmap_projection_views(rtmin, rtmax, mzmin, mzmax)
self.history.new_head((rtmin, rtmax, mzmin, mzmax))
self.update_history_entries()
def set_image_min(self, value):
self.peakmap_plotter.set_imin(value)
self.peakmap_plotter.replot()
def set_image_max(self, value):
self.peakmap_plotter.set_imax(value)
self.peakmap_plotter.replot()
def update_peakmap_projection_views(self, rtmin, rtmax, mzmin, mzmax):
rts, chroma = self.peakmap.chromatogram(mzmin, mzmax)
self.eic_plotter.del_all_items()
if self.dual_mode:
rts2, chroma2 = self.peakmap2.chromatogram(mzmin, mzmax, rtmin,
rtmax)
self.eic_plotter.add_eics([(rts, chroma), (rts2, chroma2)],
configs=[blue_line, yellow_line])
else:
self.eic_plotter.add_eics([(rts, chroma)], configs=[grey_line])
self.eic_plotter.shrink_and_replot(rtmin, rtmax)
if self.dual_mode:
data = [(self.peakmap, rtmin, rtmax, mzmin, mzmax, 3000),
(self.peakmap2, rtmin, rtmax, mzmin, mzmax, 3000)]
configs = [dict(color="#aaaa00"), dict(color="#0000aa")]
self.mz_plotter.plot_peakmaps(data, configs)
else:
self.mz_plotter.plot_peakmaps([(self.peakmap, rtmin, rtmax, mzmin,
mzmax, 3000)])
self.mz_plotter.shrink_and_replot(mzmin, mzmax)
self.view_range_widget.set_view_range(rtmin, rtmax, mzmin, mzmax)
def _handle_history_action(self, action):
item = action()
if item is not None:
self.peakmap_plotter.set_limits_no_sig(*item)
self.update_peakmap_projection_views(*item)
self.update_history_entries()
def user_pressed_left_key_in_plot(self):
self._handle_history_action(self.history.go_back)
def user_pressed_right_key_in_plot(self):
self._handle_history_action(self.history.go_forward)
def user_pressed_backspace_key_in_plot(self):
self._handle_history_action(self.history.go_to_beginning)
def user_pressed_end_key_in_plot(self):
self._handle_history_action(self.history.go_to_end)
def history_item_selected(self, index):
self._handle_history_action(
lambda index=index: self.history.set_position(index))
@protect_signal_handler
def do_save(self):
pix = self.peakmap_plotter.paint_pixmap()
while True:
path = askForSave(self.last_used_directory_for_save,
caption="Save Image",
extensions=("png", "PNG"))
if path is None:
break
__, ext = os.path.splitext(path)
if ext not in (".png", ".PNG"):
QMessageBox.warning(self, "Warning",
"wrong/missing extension '.png'")
else:
self.last_used_directory_for_save = os.path.dirname(path)
pix.save(path)
break
return
def _do_load(self, title, attribute):
path = askForSingleFile(self.last_used_directory_for_load,
caption=title,
extensions=("mzML", "mzData", "mzXML"))
if path is not None:
setattr(self, attribute, loadPeakMap(path))
self.process_peakmap()
self.peakmap_plotter.set_peakmaps(self.peakmap, self.peakmap2)
self.setup_initial_values()
self.setWindowTitle()
self.peakmap_plotter.replot()
self.plot_peakmap()
self.last_used_directory_for_load = os.path.dirname(path)
@protect_signal_handler
def do_load(self):
self._do_load("Load Peakmap", "peakmap")
@protect_signal_handler
def do_load_yellow(self):
self._do_load("Load Yellow Peakmap", "peakmap")
@protect_signal_handler
def do_load_blue(self):
self._do_load("Load Blue Peakmap", "peakmap2")
@protect_signal_handler
def select_all_peaks_button_pressed(self):
for row in range(self.table_widget.rowCount()):
item = self.table_widget.item(row, 0)
item.setCheckState(Qt.Checked)
@protect_signal_handler
def unselect_all_peaks_button_pressed(self):
for row in range(self.table_widget.rowCount()):
item = self.table_widget.item(row, 0)
item.setCheckState(Qt.Unchecked)
@protect_signal_handler
def done_button_pressed(self):
self.ok_rows[:] = [
i for i in range(len(self.table))
if self.table_widget.item(i, 0).checkState() == Qt.Checked
]
self.accept()
@protect_signal_handler
def row_selected(self, row_idx):
row = self.table.getValues(self.table.rows[row_idx])
needed = ["rtmin", "rtmax", "mzmin", "mzmax"]
if all(n in row for n in needed):
rtmin, rtmax, mzmin, mzmax = [row.get(ni) for ni in needed]
self.peakmap_plotter.set_limits(rtmin, rtmax, mzmin, mzmax)
else:
needed = ["mzmin", "mzmax"]
if all(n in row for n in needed):
mzmin, mzmax = [row.get(ni) for ni in needed]
self.peakmap_plotter.set_limits(self.rtmin, self.rtmax, mzmin,
mzmax)
@protect_signal_handler
def cell_clicked(self, item):
row = item.row()
self.table_widget.selectRow(row)
self.table_widget.verticalHeader().emit(SIGNAL("sectionClicked(int)"),
row)
@protect_signal_handler
def show_help(self):
html = resource_string("emzed.core.explorers",
"help_peakmapexplorer.html")
QWebSettings.globalSettings().setFontFamily(QWebSettings.StandardFont,
'Courier')
QWebSettings.globalSettings().setFontSize(QWebSettings.DefaultFontSize,
12)
v = QWebView(self)
v.setHtml(html)
dlg = QDialog(self, Qt.Window)
dlg.setMinimumSize(300, 300)
l = QVBoxLayout(dlg)
l.addWidget(v)
dlg.setLayout(l)
dlg.show()
def update_history_entries(self):
self.history_list.clear()
for item in self.history.items:
rtmin, rtmax, mzmin, mzmax = item
str_item = "%10.5f .. %10.5f %6.2fm...%6.2fm " % (
mzmin, mzmax, rtmin / 60.0, rtmax / 60.0)
self.history_list.addItem(str_item)
self.history_list.setCurrentIndex(self.history.position)
@protect_signal_handler
def use_logscale(self, is_log):
self.peakmap_plotter.set_logarithmic_scale(is_log)
self.peakmap_plotter.replot()
@protect_signal_handler
def ms_level_chosen(self, ms_level):
if ms_level != self.current_ms_level:
self.current_ms_level = ms_level
self.process_peakmap(ms_level)
self.peakmap_plotter.set_peakmaps(self.peakmap, self.peakmap2)
self.peakmap_plotter.replot()
self.plot_peakmap()
@protect_signal_handler
def set_precursor_range(self, pre_mz_min, pre_mz_max):
self.process_peakmap(self.current_ms_level, pre_mz_min, pre_mz_max)
self.peakmap_plotter.set_peakmaps(self.peakmap, self.peakmap2)
self.peakmap_plotter.replot()
self.plot_peakmap()
@protect_signal_handler
def gamma_changed(self, value):
self.peakmap_plotter.set_gamma(value)
self.peakmap_plotter.replot()
@protect_signal_handler
def update_image_range(self, rtmin, rtmax, mzmin, mzmax):
rtmin *= 60.0
rtmax *= 60.0
if rtmin < self.rtmin:
rtmin = self.rtmin
if rtmax > self.rtmax:
rtmax = self.rtmax
if mzmin < self.mzmin:
mzmin = self.mzmin
if mzmax > self.mzmax:
mzmax = self.mzmax
rtmin, rtmax = sorted((rtmin, rtmax))
mzmin, mzmax = sorted((mzmin, mzmax))
self.peakmap_plotter.set_limits(rtmin, rtmax, mzmin, mzmax)
def plot_peakmap(self):
self.peakmap_plotter.set_limits(self.rtmin, self.rtmax, self.mzmin,
self.mzmax)
class PeakMapExplorer(EmzedDialog):
def __init__(self, ok_rows_container=[], parent=None):
super(PeakMapExplorer, self).__init__(parent)
self.setWindowFlags(Qt.Window)
# Destroying the C++ object right after closing the dialog box,
# otherwise it may be garbage-collected in another QThread
# (e.g. the editor's analysis thread in Spyder), thus leading to
# a segmentation fault on UNIX or an application crash on Windows
self.ok_rows = ok_rows_container
self.setAttribute(Qt.WA_DeleteOnClose)
self.setWindowFlags(Qt.Window)
self.gamma = 3.0
self.last_used_directory_for_load = None
self.last_used_directory_for_save = None
self.history = History()
def keyPressEvent(self, e):
# avoid closing of dialog when Esc key pressed:
if e.key() != Qt.Key_Escape:
return super(PeakMapExplorer, self).keyPressEvent(e)
def setWindowTitle(self):
if self.peakmap2 is None:
title = os.path.basename(self.peakmap.meta.get("source", ""))
else:
p1 = os.path.basename(self.peakmap.meta.get("source", ""))
p2 = os.path.basename(self.peakmap2.meta.get("source", ""))
title = "yellow=%s, blue=%s" % (p1, p2)
super(PeakMapExplorer, self).setWindowTitle(title)
def setup(self, peakmap, peakmap2=None, table=None):
self.table = table
def collect_precursor_mz(pm):
for s in pm:
if s.precursors:
if s.msLevel > 1:
yield s.precursors[0][0]
self.ms_levels = set(peakmap.getMsLevels())
self.precursor_mz = set(collect_precursor_mz(peakmap))
if peakmap2 is not None:
self.ms_levels &= set(peakmap2.getMsLevels())
self.precursor_mz &= set(collect_precursor_mz(peakmap2))
self.ms_levels = sorted(self.ms_levels)
self.precursor_mz = sorted(self.precursor_mz)
self.setup_table_widgets()
self.setup_input_widgets()
self.history_list = QComboBox(self)
self.setup_ms2_widgets()
self.full_pm = peakmap
self.full_pm2 = peakmap2
self.dual_mode = self.full_pm2 is not None
self.current_ms_level = self.ms_levels[0]
self.process_peakmap(self.current_ms_level)
self.rtmin, self.rtmax, self.mzmin, self.mzmax = get_range(self.peakmap, self.peakmap2)
self.setup_plot_widgets()
self.setup_menu_bar()
self.setup_layout()
self.connect_signals_and_slots()
self.setup_initial_values()
self.plot_peakmap()
def setup_ms2_widgets(self):
self.spectra_selector_widget.set_data(self.ms_levels, self.precursor_mz)
def setup_table_widgets(self):
if self.table is not None:
self.table_widget = create_table_widget(self.table, self)
self.select_all_peaks = QPushButton("Select all peaks", self)
self.unselect_all_peaks = QPushButton("Unselect all peaks", self)
self.done_button = QPushButton("Done", self)
def setup_menu_bar(self):
self.menu_bar = QMenuBar(self)
menu = QMenu("Peakmap Explorer", self.menu_bar)
self.menu_bar.addMenu(menu)
if not self.dual_mode:
self.load_action = QAction("Load Peakmap", self)
self.load_action.setShortcut(QKeySequence("Ctrl+L"))
self.load_action2 = None
menu.addAction(self.load_action)
else:
self.load_action = QAction("Load Yellow Peakmap", self)
self.load_action2 = QAction("Load Blue Peakmap", self)
menu.addAction(self.load_action)
menu.addAction(self.load_action2)
self.save_action = QAction("Save selected range as image", self)
self.save_action.setShortcut(QKeySequence("Ctrl+S"))
menu.addAction(self.save_action)
menu = QMenu("Help", self.menu_bar)
self.help_action = QAction("Help", self)
self.help_action.setShortcut(QKeySequence("F1"))
menu.addAction(self.help_action)
self.menu_bar.addMenu(menu)
def process_peakmap(self, ms_level, pre_mz_min=None, pre_mz_max=None):
peakmap = self.full_pm.filter(lambda s: s.msLevel == ms_level)
if ms_level > 1 and pre_mz_min is not None:
peakmap = peakmap.filter(lambda s: s.precursors[0][0] >= pre_mz_min)
if ms_level > 1 and pre_mz_max is not None:
peakmap = peakmap.filter(lambda s: s.precursors[0][0] <= pre_mz_max)
if self.full_pm2 is not None:
peakmap2 = self.full_pm2.filter(lambda s: s.msLevel == ms_level)
self.peakmap = peakmap
if self.dual_mode:
self.peakmap2 = peakmap2
else:
self.peakmap2 = None
for i, msl in enumerate(self.ms_levels):
if msl == ms_level:
pass # TODO self.ms_level.setCurrentIndex(i)
self.setWindowTitle()
def setup_initial_values(self):
imax = self.peakmap_plotter.get_total_imax()
self.image_scaling_widget.set_max_intensity(imax)
self.image_scaling_widget.set_gamma(self.gamma)
self.view_range_widget.set_view_range(self.rtmin, self.rtmax, self.mzmin, self.mzmax)
def setup_input_widgets(self):
self.image_scaling_widget = ImageScalingWidget(self)
self.spectra_selector_widget = SpectraSelectorWidget(self)
self.view_range_widget = ViewRangeWidget(self)
def setup_plot_widgets(self):
self.peakmap_plotter = PeakMapPlottingWidget()
self.peakmap_plotter.set_peakmaps(self.peakmap, self.peakmap2)
self.eic_plotter = EicPlottingWidget(with_range=False)
self.mz_plotter = MzPlottingWidget()
self.peakmap_plotter.set_logarithmic_scale(1)
self.peakmap_plotter.set_gamma(self.gamma)
self.eic_plotter.set_overall_range(self.rtmin, self.rtmax)
self.mz_plotter.set_overall_range(self.mzmin, self.mzmax)
def setup_layout(self):
outer_layout = QVBoxLayout()
outer_layout.addWidget(self.menu_bar)
outer_layout.setStretch(0, 1)
h_splitter = QSplitter(self)
h_splitter.setOrientation(Qt.Horizontal)
# FIRST COLUMN of h_splitter is chromatogram + peakmap: ############################
v_splitter1 = QSplitter(self)
v_splitter1.setOrientation(Qt.Vertical)
v_splitter1.addWidget(self.eic_plotter)
v_splitter1.addWidget(self.peakmap_plotter)
self.peakmap_plotter.setMinimumSize(250, 200)
v_splitter1.setStretchFactor(0, 1)
v_splitter1.setStretchFactor(1, 3)
h_splitter.addWidget(v_splitter1)
h_splitter.setStretchFactor(0, 2)
# SECOND COLUMN of h_splittier holds controlx boxes + mz plot #######################
v_splitter2 = QSplitter(self)
v_splitter2.setOrientation(Qt.Vertical)
v_splitter2.addWidget(self.image_scaling_widget)
v_splitter2.addWidget(self.spectra_selector_widget)
v_splitter2.addWidget(self.view_range_widget)
v_splitter2.addWidget(self.history_list)
v_splitter2.addWidget(self.mz_plotter)
v_splitter2.setStretchFactor(0, 0)
v_splitter2.setStretchFactor(1, 0)
v_splitter2.setStretchFactor(2, 0)
v_splitter2.setStretchFactor(3, 0)
v_splitter2.setStretchFactor(4, 1)
h_splitter.addWidget(v_splitter2)
h_splitter.setStretchFactor(1, 1)
# THIRD COLUMN of h_splittier holds control table + buttons ##########################
if self.table:
frame = QFrame(self)
layout = QVBoxLayout(frame)
frame.setLayout(layout)
layout.addWidget(self.table_widget)
button_row_layout = QHBoxLayout(frame)
button_row_layout.addWidget(self.select_all_peaks)
button_row_layout.addWidget(self.unselect_all_peaks)
button_row_layout.addWidget(self.done_button)
layout.addLayout(button_row_layout)
h_splitter.addWidget(frame)
h_splitter.setStretchFactor(2, 2)
outer_layout.addWidget(h_splitter)
self.setLayout(outer_layout)
outer_layout.setStretch(1, 99)
def connect_signals_and_slots(self):
self.image_scaling_widget.USE_LOG_SCALE.connect(self.use_logscale)
self.image_scaling_widget.GAMMA_CHANGED.connect(self.gamma_changed)
self.image_scaling_widget.IMIN_CHANGED.connect(self.set_image_min)
self.image_scaling_widget.IMAX_CHANGED.connect(self.set_image_max)
self.spectra_selector_widget.MS_LEVEL_CHOSEN.connect(self.ms_level_chosen)
self.spectra_selector_widget.PRECURSOR_RANGE_CHANGED.connect(self.set_precursor_range)
self.view_range_widget.RANGE_CHANGED.connect(self.update_image_range)
self.connect(self.history_list, SIGNAL("activated(int)"), self.history_item_selected)
if self.dual_mode:
self.connect(self.load_action, SIGNAL("triggered()"), self.do_load_yellow)
self.connect(self.load_action2, SIGNAL("triggered()"), self.do_load_blue)
else:
self.connect(self.load_action, SIGNAL("triggered()"), self.do_load)
self.connect(self.save_action, SIGNAL("triggered()"), self.do_save)
self.connect(self.help_action, SIGNAL("triggered()"), self.show_help)
self.peakmap_plotter.NEW_IMAGE_LIMITS.connect(self.image_limits_upated_by_user)
self.peakmap_plotter.KEY_LEFT.connect(self.user_pressed_left_key_in_plot)
self.peakmap_plotter.KEY_RIGHT.connect(self.user_pressed_right_key_in_plot)
self.peakmap_plotter.KEY_BACKSPACE.connect(self.user_pressed_backspace_key_in_plot)
self.peakmap_plotter.KEY_END.connect(self.user_pressed_end_key_in_plot)
self.peakmap_plotter.CURSOR_MOVED.connect(self.cursor_moved_in_plot)
self.eic_plotter.CURSOR_MOVED.connect(self.eic_cursor_moved)
self.eic_plotter.VIEW_RANGE_CHANGED.connect(self.eic_view_range_changed)
self.mz_plotter.CURSOR_MOVED.connect(self.mz_cursor_moved)
self.mz_plotter.VIEW_RANGE_CHANGED.connect(self.mz_view_range_changed)
if self.table is not None:
self.connect(self.table_widget.verticalHeader(), SIGNAL("sectionClicked(int)"),
self.row_selected)
self.connect(self.table_widget, SIGNAL("itemClicked(QTableWidgetItem*)"),
self.cell_clicked)
self.connect(self.select_all_peaks, SIGNAL("pressed()"),
self.select_all_peaks_button_pressed)
self.connect(self.unselect_all_peaks, SIGNAL("pressed()"),
self.unselect_all_peaks_button_pressed)
self.connect(self.done_button, SIGNAL("pressed()"),
self.done_button_pressed)
def key_release_handler(evt):
tw = self.table_widget
active_rows = set(ix.row() for ix in tw.selectionModel().selection().indexes())
if active_rows:
row = active_rows.pop()
if evt.key() in (Qt.Key_Up, Qt.Key_Down):
tw.selectRow(row)
tw.verticalHeader().emit(SIGNAL("sectionClicked(int)"), row)
return
return QTableWidget.keyPressEvent(tw, evt)
self.table_widget.keyReleaseEvent = key_release_handler
def cursor_moved_in_plot(self, rt, mz):
self.eic_plotter.set_cursor_pos(rt)
self.mz_plotter.set_cursor_pos(mz)
def eic_cursor_moved(self, rt):
self.peakmap_plotter.set_cursor_rt(rt)
def eic_view_range_changed(self, rtmin, rtmax):
"""
we want to avoid the loop EIC_RANGE_CHANGED -> VIEW_RANGE_CHANGED -> EIC_RANGE_CHANGED
and we do not want to fully block emitting of VIEW_RANGE_CHANGED.
so self.peakmap_plotter.blockSignals() does not work here, instead we "cut" the last
connection here:
"""
self.eic_plotter.VIEW_RANGE_CHANGED.disconnect()
self.peakmap_plotter.blockSignals(True)
self.peakmap_plotter.set_rt_limits(rtmin, rtmax)
self.peakmap_plotter.blockSignals(False)
self.peakmap_plotter.replot()
self.eic_plotter.VIEW_RANGE_CHANGED.connect(self.eic_view_range_changed)
def mz_view_range_changed(self, mzmin, mzmax):
"""
we want to avoid the loop MZ_RANGE_CHANGED -> VIEW_RANGE_CHANGED -> MZ_RANGE_CHANGED
and we do not want to fully block emitting of VIEW_RANGE_CHANGED.
so self.peakmap_plotter.blockSignals() does not work here, instead we "cut" the last
connection here:
"""
self.mz_plotter.VIEW_RANGE_CHANGED.disconnect()
self.peakmap_plotter.blockSignals(True)
self.peakmap_plotter.set_mz_limits(mzmin, mzmax)
self.peakmap_plotter.blockSignals(False)
self.peakmap_plotter.replot()
self.mz_plotter.VIEW_RANGE_CHANGED.connect(self.mz_view_range_changed)
def mz_cursor_moved(self, mz):
self.peakmap_plotter.set_cursor_mz(mz)
def image_limits_upated_by_user(self, rtmin, rtmax, mzmin, mzmax):
self.update_peakmap_projection_views(rtmin, rtmax, mzmin, mzmax)
self.history.new_head((rtmin, rtmax, mzmin, mzmax))
self.update_history_entries()
def set_image_min(self, value):
self.peakmap_plotter.set_imin(value)
self.peakmap_plotter.replot()
def set_image_max(self, value):
self.peakmap_plotter.set_imax(value)
self.peakmap_plotter.replot()
def update_peakmap_projection_views(self, rtmin, rtmax, mzmin, mzmax):
rts, chroma = self.peakmap.chromatogram(mzmin, mzmax)
self.eic_plotter.del_all_items()
if self.dual_mode:
rts2, chroma2 = self.peakmap2.chromatogram(mzmin, mzmax, rtmin, rtmax)
self.eic_plotter.add_eics([(rts, chroma), (rts2, chroma2)], configs=[blue_line, yellow_line])
else:
self.eic_plotter.add_eics([(rts, chroma)], configs=[grey_line])
self.eic_plotter.shrink_and_replot(rtmin, rtmax)
if self.dual_mode:
data = [(self.peakmap, rtmin, rtmax, mzmin, mzmax, 3000),
(self.peakmap2, rtmin, rtmax, mzmin, mzmax, 3000)]
configs = [dict(color="#aaaa00"), dict(color="#0000aa")]
self.mz_plotter.plot_peakmaps(data, configs)
else:
self.mz_plotter.plot_peakmaps([(self.peakmap, rtmin, rtmax, mzmin, mzmax, 3000)])
self.mz_plotter.shrink_and_replot(mzmin, mzmax)
self.view_range_widget.set_view_range(rtmin, rtmax, mzmin, mzmax)
def _handle_history_action(self, action):
item = action()
if item is not None:
self.peakmap_plotter.set_limits_no_sig(*item)
self.update_peakmap_projection_views(*item)
self.update_history_entries()
def user_pressed_left_key_in_plot(self):
self._handle_history_action(self.history.go_back)
def user_pressed_right_key_in_plot(self):
self._handle_history_action(self.history.go_forward)
def user_pressed_backspace_key_in_plot(self):
self._handle_history_action(self.history.go_to_beginning)
def user_pressed_end_key_in_plot(self):
self._handle_history_action(self.history.go_to_end)
def history_item_selected(self, index):
self._handle_history_action(lambda index=index: self.history.set_position(index))
@protect_signal_handler
def do_save(self):
pix = self.peakmap_plotter.paint_pixmap()
while True:
path = askForSave(self.last_used_directory_for_save,
caption="Save Image",
extensions=("png", "PNG")
)
if path is None:
break
__, ext = os.path.splitext(path)
if ext not in (".png", ".PNG"):
QMessageBox.warning(self, "Warning", "wrong/missing extension '.png'")
else:
self.last_used_directory_for_save = os.path.dirname(path)
pix.save(path)
break
return
def _do_load(self, title, attribute):
path = askForSingleFile(self.last_used_directory_for_load,
caption=title,
extensions=("mzML", "mzData", "mzXML")
)
if path is not None:
setattr(self, attribute, loadPeakMap(path))
self.process_peakmap()
self.peakmap_plotter.set_peakmaps(self.peakmap, self.peakmap2)
self.setup_initial_values()
self.setWindowTitle()
self.peakmap_plotter.replot()
self.plot_peakmap()
self.last_used_directory_for_load = os.path.dirname(path)
@protect_signal_handler
def do_load(self):
self._do_load("Load Peakmap", "peakmap")
@protect_signal_handler
def do_load_yellow(self):
self._do_load("Load Yellow Peakmap", "peakmap")
@protect_signal_handler
def do_load_blue(self):
self._do_load("Load Blue Peakmap", "peakmap2")
@protect_signal_handler
def select_all_peaks_button_pressed(self):
for row in range(self.table_widget.rowCount()):
item = self.table_widget.item(row, 0)
item.setCheckState(Qt.Checked)
@protect_signal_handler
def unselect_all_peaks_button_pressed(self):
for row in range(self.table_widget.rowCount()):
item = self.table_widget.item(row, 0)
item.setCheckState(Qt.Unchecked)
@protect_signal_handler
def done_button_pressed(self):
self.ok_rows[:] = [i for i in range(len(self.table))
if self.table_widget.item(i, 0).checkState() == Qt.Checked]
self.accept()
@protect_signal_handler
def row_selected(self, row_idx):
row = self.table.getValues(self.table.rows[row_idx])
needed = ["rtmin", "rtmax", "mzmin", "mzmax"]
if all(n in row for n in needed):
rtmin, rtmax, mzmin, mzmax = [row.get(ni) for ni in needed]
self.peakmap_plotter.set_limits(rtmin, rtmax, mzmin, mzmax)
else:
needed = ["mzmin", "mzmax"]
if all(n in row for n in needed):
mzmin, mzmax = [row.get(ni) for ni in needed]
self.peakmap_plotter.set_limits(self.rtmin, self.rtmax, mzmin, mzmax)
@protect_signal_handler
def cell_clicked(self, item):
row = item.row()
self.table_widget.selectRow(row)
self.table_widget.verticalHeader().emit(SIGNAL("sectionClicked(int)"), row)
@protect_signal_handler
def show_help(self):
html = resource_string("emzed.core.explorers", "help_peakmapexplorer.html")
QWebSettings.globalSettings().setFontFamily(QWebSettings.StandardFont, 'Courier')
QWebSettings.globalSettings().setFontSize(QWebSettings.DefaultFontSize, 12)
v = QWebView(self)
v.setHtml(html)
dlg = QDialog(self, Qt.Window)
dlg.setMinimumSize(300, 300)
l = QVBoxLayout(dlg)
l.addWidget(v)
dlg.setLayout(l)
dlg.show()
def update_history_entries(self):
self.history_list.clear()
for item in self.history.items:
rtmin, rtmax, mzmin, mzmax = item
str_item = "%10.5f .. %10.5f %6.2fm...%6.2fm " % (mzmin, mzmax, rtmin / 60.0,
rtmax / 60.0)
self.history_list.addItem(str_item)
self.history_list.setCurrentIndex(self.history.position)
@protect_signal_handler
def use_logscale(self, is_log):
self.peakmap_plotter.set_logarithmic_scale(is_log)
self.peakmap_plotter.replot()
@protect_signal_handler
def ms_level_chosen(self, ms_level):
if ms_level != self.current_ms_level:
self.current_ms_level = ms_level
self.process_peakmap(ms_level)
self.peakmap_plotter.set_peakmaps(self.peakmap, self.peakmap2)
self.peakmap_plotter.replot()
self.plot_peakmap()
@protect_signal_handler
def set_precursor_range(self, pre_mz_min, pre_mz_max):
self.process_peakmap(self.current_ms_level, pre_mz_min, pre_mz_max)
self.peakmap_plotter.set_peakmaps(self.peakmap, self.peakmap2)
self.peakmap_plotter.replot()
self.plot_peakmap()
@protect_signal_handler
def gamma_changed(self, value):
self.peakmap_plotter.set_gamma(value)
self.peakmap_plotter.replot()
@protect_signal_handler
def update_image_range(self, rtmin, rtmax, mzmin, mzmax):
rtmin *= 60.0
rtmax *= 60.0
if rtmin < self.rtmin:
rtmin = self.rtmin
if rtmax > self.rtmax:
rtmax = self.rtmax
if mzmin < self.mzmin:
mzmin = self.mzmin
if mzmax > self.mzmax:
mzmax = self.mzmax
rtmin, rtmax = sorted((rtmin, rtmax))
mzmin, mzmax = sorted((mzmin, mzmax))
self.peakmap_plotter.set_limits(rtmin, rtmax, mzmin, mzmax)
def plot_peakmap(self):
self.peakmap_plotter.set_limits(self.rtmin, self.rtmax, self.mzmin, self.mzmax)
